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Open data
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Basic information
Entry | Database: PDB / ID: 4s3c | ||||||
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Title | IspG in complex with Epoxide Intermediate | ||||||
![]() | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase | ||||||
![]() | OXIDOREDUCTASE / Methylerythritol-Phosphate Pathway / Terpene Biosynthesis / Iron-Sulfur Enzymes / Reaction Mechanisms / Drug Development | ||||||
Function / homology | ![]() (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase (flavodoxin) / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity (ferredoxin) / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 4 iron, 4 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Quitterer, F. / Frank, A. / Wang, K. / Rao, G. / O'Dowd, B. / Li, J. / Guerra, F. / Abdel-Azeim, S. / Bacher, A. / Eppinger, J. ...Quitterer, F. / Frank, A. / Wang, K. / Rao, G. / O'Dowd, B. / Li, J. / Guerra, F. / Abdel-Azeim, S. / Bacher, A. / Eppinger, J. / Oldfield, E. / Groll, M. | ||||||
![]() | ![]() Title: Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE). Authors: Quitterer, F. / Frank, A. / Wang, K. / Rao, G. / O'Dowd, B. / Li, J. / Guerra, F. / Abdel-Azeim, S. / Bacher, A. / Eppinger, J. / Oldfield, E. / Groll, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187 KB | Display | ![]() |
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PDB format | ![]() | 147.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4s38SC ![]() 4s39C ![]() 4s3aC ![]() 4s3bC ![]() 4s3dC ![]() 4s3eC ![]() 4s3fC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 44278.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-43Q / ( |
#3: Chemical | ChemComp-SF4 / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BIS-TRIS PROPANE; 20% PEG3350; 0.2 M Na2SO4 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2014 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.971 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30 Å / Num. all: 84126 / Num. obs: 81686 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.45→1.55 Å / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.4 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4S38 Resolution: 1.45→10 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.979 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→10 Å
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Refine LS restraints |
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